Objective To explore the changing trend of the incidence of singleton small vulnerable neonates (SVN) and its influencing factors, and to analyze the association between parental factors and SVN. Methods A retrospective cohort study was conducted, recruiting 13,020 pregnant women who established prenatal records before 14 weeks of gestation between January 2019 and December 2023 and received standardized antenatal care until delivery. Based on neonatal outcomes, those meeting the SVN criteria were assigned to the SVN group, with the remaining assigned to the control group. SVN encompassed three phenotypes: preterm birth (PT), small for gestational age (SGA), and low birth weight (LBW). Baseline maternal characteristics, pregnancy complications, paternal anthropometric parameters, and pregnancy outcomes were compared between the two groups. Logistic regression analysis was employed to identify parental influencing factors for SVN. Results During the study period, the overall SVN incidence was 12.73% (1658/13020), comprising PT (3.16%, 412/13020), LBW (2.53%, 329/13020), and SGA (9.57%, 1246/13020). The incidence rates of PT and LBW decreased by 49.12% and 29.73% respectively in 2023 compared with 2019, but the incidence rate of SGA increased by 37.04% in 2023 compared with 2019. Among all pregnant women, the Zhuang ethnic group accounted for 37.55% of all ethnic groups, those with a bachelor's degree or above accounted for 82.33%, and multiparous women accounted for 48.21%. A total of 719 pregnant women (5.52%) had a history of diseases before pregnancy, and abnormal thyroid function was the most common (4.21%, 548/13020). A total of 3,582 pregnant women underwent pre-pregnancy genetic testing related to thalassemia, and 1,864 cases were detected positive (detection rate 52.04%), among which the detection rate of alpha thalassemia minor was the highest (674 cases, 18.82%). The proportion of fathers aged 35 or above was 37.08%, while the proportion of those who were overweight or obese (BMI ≥ 24 kg/m²) was 50.53%, and the proportion of those who were underweight was only 2.73%. Multivariate logistic regression analysis revealed that maternal pre-pregnancy overweight, multiparity, and AB blood type were protective factors for SVN (P<0.05); whereas maternal pre-pregnancy underweight, pregnancy complicated by polycystic ovarian syndrome (PCOS), and gestational hypertensive disorders (HDP) were identified as risk factors for SVN (P<0.05). Neonates in the SVN group exhibited significantly smaller gestational age, shorter body length, lower birth weight, and higher rates of neonatal asphyxia and mortality, with statistically significant differences (P<0.05). Conclusions The three phenotypic subtypes of SVN exhibited divergent incidence trends over the five-year period, with the incidence of SGA demonstrating an upward trajectory warranting focused attention. The occurrence of SVN showed strong associations with maternal pre-pregnancy nutritional status, comorbid PCOS, and HDP, highlighting the necessity for enhancing antenatal care and preventing HDP during pregnancy. This study did not identify significant impacts of paternal age or BMI on SVN.